adjust_matrix {cola} | R Documentation

## Remove rows with low variance and impute missing values

### Description

Remove rows with low variance and impute missing values

### Usage

    adjust_matrix(m, sd_quantile = 0.05, max_na = 0.25)

### Arguments

`m` | A numeric matrix.
`sd_quantile` | Cutoff of the quantile of standard deviation. Rows with standard deviation less than it are removed.
`max_na` | Maximum NA fraction in each row. Rows with NA fraction larger than it are removed.

### Details

The function uses `impute.knn` to impute missing values, then uses `adjust_outlier` to adjust outliers and removes rows with low standard deviations.

### Value

A numeric matrix.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### Examples

    m = matrix(rnorm(200), 10)
    rownames(m) = letters[1:10]
    m[1, 1] = 1000
    range(m)
    m2 = adjust_matrix(m)
    range(m2)

[Package cola version 1.2.1 Index]